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_mnt_d_Github_synthpops_synthpops_read_write_py.html
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<!DOCTYPE html>
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<title>Coverage for /mnt/d/Github/synthpops/synthpops/read_write.py: 47%</title>
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<h1>Coverage for <b>/mnt/d/Github/synthpops/synthpops/read_write.py</b> :
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<p id="t1" class="pln"><span class="n"><a href="#t1">1</a></span><span class="t"><span class="str">"""</span> </span><span class="r"></span></p>
<p id="t2" class="pln"><span class="n"><a href="#t2">2</a></span><span class="t"><span class="str">This module contains reading and writing functions for contact networks and populations</span> </span><span class="r"></span></p>
<p id="t3" class="pln"><span class="n"><a href="#t3">3</a></span><span class="t"><span class="str">"""</span> </span><span class="r"></span></p>
<p id="t4" class="pln"><span class="n"><a href="#t4">4</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t5" class="run"><span class="n"><a href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">os</span> </span><span class="r"></span></p>
<p id="t6" class="pln"><span class="n"><a href="#t6">6</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t7" class="run"><span class="n"><a href="#t7">7</a></span><span class="t"><span class="key">import</span> <span class="nam">sciris</span> <span class="key">as</span> <span class="nam">sc</span> </span><span class="r"></span></p>
<p id="t8" class="run"><span class="n"><a href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span> </span><span class="r"></span></p>
<p id="t9" class="run"><span class="n"><a href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span> </span><span class="r"></span></p>
<p id="t10" class="pln"><span class="n"><a href="#t10">10</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t11" class="pln"><span class="n"><a href="#t11">11</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t12" class="run"><span class="n"><a href="#t12">12</a></span><span class="t"><span class="key">def</span> <span class="nam">write_age_by_uid_dic</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">,</span> <span class="nam">age_by_uid_dic</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t13" class="pln"><span class="n"><a href="#t13">13</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t14" class="pln"><span class="n"><a href="#t14">14</a></span><span class="t"><span class="str"> Write the dictionary of ID mapping to age for each individual in the population.</span> </span><span class="r"></span></p>
<p id="t15" class="pln"><span class="n"><a href="#t15">15</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t16" class="pln"><span class="n"><a href="#t16">16</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t17" class="pln"><span class="n"><a href="#t17">17</a></span><span class="t"><span class="str"> datadir (string) : The file path to the data directory.</span> </span><span class="r"></span></p>
<p id="t18" class="pln"><span class="n"><a href="#t18">18</a></span><span class="t"><span class="str"> location (string) : The name of the location.</span> </span><span class="r"></span></p>
<p id="t19" class="pln"><span class="n"><a href="#t19">19</a></span><span class="t"><span class="str"> state_location (string) : The name of the state the location is in.</span> </span><span class="r"></span></p>
<p id="t20" class="pln"><span class="n"><a href="#t20">20</a></span><span class="t"><span class="str"> country_location (string) : The name of the country the location is in.</span> </span><span class="r"></span></p>
<p id="t21" class="pln"><span class="n"><a href="#t21">21</a></span><span class="t"><span class="str"> folder_name (string) : The name of the folder the location is in, e.g. 'contact_networks'</span> </span><span class="r"></span></p>
<p id="t22" class="pln"><span class="n"><a href="#t22">22</a></span><span class="t"><span class="str"> age_by_uid_dic (dict) : A dictionary mapping ID to age for each individual in the population.</span> </span><span class="r"></span></p>
<p id="t23" class="pln"><span class="n"><a href="#t23">23</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t24" class="pln"><span class="n"><a href="#t24">24</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t25" class="pln"><span class="n"><a href="#t25">25</a></span><span class="t"><span class="str"> None</span> </span><span class="r"></span></p>
<p id="t26" class="pln"><span class="n"><a href="#t26">26</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t27" class="pln"><span class="n"><a href="#t27">27</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t28" class="mis show_mis"><span class="n"><a href="#t28">28</a></span><span class="t"> <span class="nam">file_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="str">'demographics'</span><span class="op">,</span> <span class="str">'contact_matrices_152_countries'</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t29" class="mis show_mis"><span class="n"><a href="#t29">29</a></span><span class="t"> <span class="nam">os</span><span class="op">.</span><span class="nam">makedirs</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">exist_ok</span><span class="op">=</span><span class="key">True</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t30" class="pln"><span class="n"><a href="#t30">30</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t31" class="mis show_mis"><span class="n"><a href="#t31">31</a></span><span class="t"> <span class="nam">age_by_uid_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">age_by_uid_dic</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_age_by_uid.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t32" class="pln"><span class="n"><a href="#t32">32</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t33" class="mis show_mis"><span class="n"><a href="#t33">33</a></span><span class="t"> <span class="nam">f_age_uid</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">age_by_uid_path</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t34" class="pln"><span class="n"><a href="#t34">34</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t35" class="mis show_mis"><span class="n"><a href="#t35">35</a></span><span class="t"> <span class="nam">uids</span> <span class="op">=</span> <span class="nam">sorted</span><span class="op">(</span><span class="nam">age_by_uid_dic</span><span class="op">.</span><span class="nam">keys</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t36" class="mis show_mis"><span class="n"><a href="#t36">36</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">uids</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t37" class="mis show_mis"><span class="n"><a href="#t37">37</a></span><span class="t"> <span class="nam">f_age_uid</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">str</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">age_by_uid_dic</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">)</span> <span class="op">+</span> <span class="str">'\n'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t38" class="mis show_mis"><span class="n"><a href="#t38">38</a></span><span class="t"> <span class="nam">f_age_uid</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t39" class="pln"><span class="n"><a href="#t39">39</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t40" class="pln"><span class="n"><a href="#t40">40</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t41" class="run"><span class="n"><a href="#t41">41</a></span><span class="t"><span class="key">def</span> <span class="nam">read_in_age_by_uid</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">,</span> <span class="nam">n</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t42" class="pln"><span class="n"><a href="#t42">42</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t43" class="pln"><span class="n"><a href="#t43">43</a></span><span class="t"><span class="str"> Read dictionary of ID mapping to ages for all individuals from file.</span> </span><span class="r"></span></p>
<p id="t44" class="pln"><span class="n"><a href="#t44">44</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t45" class="pln"><span class="n"><a href="#t45">45</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t46" class="pln"><span class="n"><a href="#t46">46</a></span><span class="t"><span class="str"> datadir (string) : The file path to the data directory.</span> </span><span class="r"></span></p>
<p id="t47" class="pln"><span class="n"><a href="#t47">47</a></span><span class="t"><span class="str"> location (string) : The name of the location.</span> </span><span class="r"></span></p>
<p id="t48" class="pln"><span class="n"><a href="#t48">48</a></span><span class="t"><span class="str"> state_location (string) : The name of the state the location is in.</span> </span><span class="r"></span></p>
<p id="t49" class="pln"><span class="n"><a href="#t49">49</a></span><span class="t"><span class="str"> country_location (string) : The name of the country the location is in.</span> </span><span class="r"></span></p>
<p id="t50" class="pln"><span class="n"><a href="#t50">50</a></span><span class="t"><span class="str"> folder_name (string) : The name of the folder the location is in, e.g. 'contact_networks'</span> </span><span class="r"></span></p>
<p id="t51" class="pln"><span class="n"><a href="#t51">51</a></span><span class="t"><span class="str"> n (int) : The number of people in the population.</span> </span><span class="r"></span></p>
<p id="t52" class="pln"><span class="n"><a href="#t52">52</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t53" class="pln"><span class="n"><a href="#t53">53</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t54" class="pln"><span class="n"><a href="#t54">54</a></span><span class="t"><span class="str"> A dictionary mapping ID to age for all individuals in the population.</span> </span><span class="r"></span></p>
<p id="t55" class="pln"><span class="n"><a href="#t55">55</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t56" class="pln"><span class="n"><a href="#t56">56</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t57" class="run"><span class="n"><a href="#t57">57</a></span><span class="t"> <span class="nam">file_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="str">'demographics'</span><span class="op">,</span> <span class="str">'contact_matrices_152_countries'</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t58" class="run"><span class="n"><a href="#t58">58</a></span><span class="t"> <span class="nam">age_by_uid_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_age_by_uid.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t59" class="run"><span class="n"><a href="#t59">59</a></span><span class="t"> <span class="nam">df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">read_csv</span><span class="op">(</span><span class="nam">age_by_uid_path</span><span class="op">,</span> <span class="nam">header</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">delimiter</span><span class="op">=</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t60" class="run"><span class="n"><a href="#t60">60</a></span><span class="t"> <span class="key">try</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t61" class="run"><span class="n"><a href="#t61">61</a></span><span class="t"> <span class="key">return</span> <span class="nam">dict</span><span class="op">(</span><span class="nam">zip</span><span class="op">(</span><span class="nam">df</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span><span class="op">.</span><span class="nam">values</span><span class="op">.</span><span class="nam">astype</span><span class="op">(</span><span class="nam">int</span><span class="op">)</span><span class="op">,</span> <span class="nam">df</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">.</span><span class="nam">values</span><span class="op">.</span><span class="nam">astype</span><span class="op">(</span><span class="nam">int</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t62" class="mis show_mis"><span class="n"><a href="#t62">62</a></span><span class="t"> <span class="key">except</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t63" class="mis show_mis"><span class="n"><a href="#t63">63</a></span><span class="t"> <span class="key">return</span> <span class="nam">dict</span><span class="op">(</span><span class="nam">zip</span><span class="op">(</span><span class="nam">df</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span><span class="op">.</span><span class="nam">values</span><span class="op">,</span> <span class="nam">df</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">.</span><span class="nam">values</span><span class="op">.</span><span class="nam">astype</span><span class="op">(</span><span class="nam">int</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t64" class="pln"><span class="n"><a href="#t64">64</a></span><span class="t"> <span class="com"># return sc.objdict(zip(df.iloc[:, 0].values, df.iloc[:, 1].values.astype(int)))</span> </span><span class="r"></span></p>
<p id="t65" class="pln"><span class="n"><a href="#t65">65</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t66" class="pln"><span class="n"><a href="#t66">66</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t67" class="run"><span class="n"><a href="#t67">67</a></span><span class="t"><span class="key">def</span> <span class="nam">write_groups_by_age_and_uid</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">,</span> <span class="nam">age_by_uid_dic</span><span class="op">,</span> <span class="nam">group_type</span><span class="op">,</span> <span class="nam">groups_by_uids</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t68" class="pln"><span class="n"><a href="#t68">68</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t69" class="pln"><span class="n"><a href="#t69">69</a></span><span class="t"><span class="str"> Write groups to file with both ID and their ages.</span> </span><span class="r"></span></p>
<p id="t70" class="pln"><span class="n"><a href="#t70">70</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t71" class="pln"><span class="n"><a href="#t71">71</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t72" class="pln"><span class="n"><a href="#t72">72</a></span><span class="t"><span class="str"> datadir (string) : The file path to the data directory.</span> </span><span class="r"></span></p>
<p id="t73" class="pln"><span class="n"><a href="#t73">73</a></span><span class="t"><span class="str"> location (string) : The name of the location.</span> </span><span class="r"></span></p>
<p id="t74" class="pln"><span class="n"><a href="#t74">74</a></span><span class="t"><span class="str"> state_location (string) : The name of the state of the location is in.</span> </span><span class="r"></span></p>
<p id="t75" class="pln"><span class="n"><a href="#t75">75</a></span><span class="t"><span class="str"> country_location (string) : The name of the country the location is in.</span> </span><span class="r"></span></p>
<p id="t76" class="pln"><span class="n"><a href="#t76">76</a></span><span class="t"><span class="str"> folder_name (string) : The name of the folder the location is in, e.g. 'contact_networks'</span> </span><span class="r"></span></p>
<p id="t77" class="pln"><span class="n"><a href="#t77">77</a></span><span class="t"><span class="str"> age_by_uid_dic (dict) : A dictionary mapping ID to age for each individual in the population.</span> </span><span class="r"></span></p>
<p id="t78" class="pln"><span class="n"><a href="#t78">78</a></span><span class="t"><span class="str"> group_type (string) : The name of the group type.</span> </span><span class="r"></span></p>
<p id="t79" class="pln"><span class="n"><a href="#t79">79</a></span><span class="t"><span class="str"> groups_by_uids (list) : The list of lists, where each sublist represents a household and the IDs of the household members.</span> </span><span class="r"></span></p>
<p id="t80" class="pln"><span class="n"><a href="#t80">80</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t81" class="pln"><span class="n"><a href="#t81">81</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t82" class="pln"><span class="n"><a href="#t82">82</a></span><span class="t"><span class="str"> None</span> </span><span class="r"></span></p>
<p id="t83" class="pln"><span class="n"><a href="#t83">83</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t84" class="pln"><span class="n"><a href="#t84">84</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t85" class="mis show_mis"><span class="n"><a href="#t85">85</a></span><span class="t"> <span class="nam">file_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="str">'demographics'</span><span class="op">,</span> <span class="str">'contact_matrices_152_countries'</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t86" class="mis show_mis"><span class="n"><a href="#t86">86</a></span><span class="t"> <span class="nam">os</span><span class="op">.</span><span class="nam">makedirs</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">exist_ok</span><span class="op">=</span><span class="key">True</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t87" class="pln"><span class="n"><a href="#t87">87</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t88" class="mis show_mis"><span class="n"><a href="#t88">88</a></span><span class="t"> <span class="nam">groups_by_age_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">age_by_uid_dic</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_'</span> <span class="op">+</span> <span class="nam">group_type</span> <span class="op">+</span> <span class="str">'_with_ages.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t89" class="mis show_mis"><span class="n"><a href="#t89">89</a></span><span class="t"> <span class="nam">groups_by_uid_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">age_by_uid_dic</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_'</span> <span class="op">+</span> <span class="nam">group_type</span> <span class="op">+</span> <span class="str">'_with_uids.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t90" class="pln"><span class="n"><a href="#t90">90</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t91" class="mis show_mis"><span class="n"><a href="#t91">91</a></span><span class="t"> <span class="nam">fg_age</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">groups_by_age_path</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t92" class="mis show_mis"><span class="n"><a href="#t92">92</a></span><span class="t"> <span class="nam">fg_uid</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">groups_by_uid_path</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t93" class="pln"><span class="n"><a href="#t93">93</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t94" class="mis show_mis"><span class="n"><a href="#t94">94</a></span><span class="t"> <span class="key">for</span> <span class="nam">n</span><span class="op">,</span> <span class="nam">ids</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">groups_by_uids</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t95" class="pln"><span class="n"><a href="#t95">95</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t96" class="mis show_mis"><span class="n"><a href="#t96">96</a></span><span class="t"> <span class="nam">group</span> <span class="op">=</span> <span class="nam">groups_by_uids</span><span class="op">[</span><span class="nam">n</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t97" class="pln"><span class="n"><a href="#t97">97</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t98" class="mis show_mis"><span class="n"><a href="#t98">98</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">group</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t99" class="pln"><span class="n"><a href="#t99">99</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t100" class="mis show_mis"><span class="n"><a href="#t100">100</a></span><span class="t"> <span class="nam">fg_age</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">str</span><span class="op">(</span><span class="nam">int</span><span class="op">(</span><span class="nam">age_by_uid_dic</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t101" class="mis show_mis"><span class="n"><a href="#t101">101</a></span><span class="t"> <span class="nam">fg_uid</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">str</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t102" class="mis show_mis"><span class="n"><a href="#t102">102</a></span><span class="t"> <span class="nam">fg_age</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'\n'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t103" class="mis show_mis"><span class="n"><a href="#t103">103</a></span><span class="t"> <span class="nam">fg_uid</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'\n'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t104" class="mis show_mis"><span class="n"><a href="#t104">104</a></span><span class="t"> <span class="nam">fg_age</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t105" class="mis show_mis"><span class="n"><a href="#t105">105</a></span><span class="t"> <span class="nam">fg_uid</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t106" class="pln"><span class="n"><a href="#t106">106</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t107" class="pln"><span class="n"><a href="#t107">107</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t108" class="run"><span class="n"><a href="#t108">108</a></span><span class="t"><span class="key">def</span> <span class="nam">read_setting_groups</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">,</span> <span class="nam">group_type</span><span class="op">,</span> <span class="nam">n</span><span class="op">,</span> <span class="nam">with_ages</span><span class="op">=</span><span class="key">False</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t109" class="pln"><span class="n"><a href="#t109">109</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t110" class="pln"><span class="n"><a href="#t110">110</a></span><span class="t"><span class="str"> Read in groups of people interacting in different social settings from file.</span> </span><span class="r"></span></p>
<p id="t111" class="pln"><span class="n"><a href="#t111">111</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t112" class="pln"><span class="n"><a href="#t112">112</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t113" class="pln"><span class="n"><a href="#t113">113</a></span><span class="t"><span class="str"> datadir (string) : The file path to the data directory.</span> </span><span class="r"></span></p>
<p id="t114" class="pln"><span class="n"><a href="#t114">114</a></span><span class="t"><span class="str"> location (string) : The name of the location.</span> </span><span class="r"></span></p>
<p id="t115" class="pln"><span class="n"><a href="#t115">115</a></span><span class="t"><span class="str"> state_location (string) : The name of the state the location is in.</span> </span><span class="r"></span></p>
<p id="t116" class="pln"><span class="n"><a href="#t116">116</a></span><span class="t"><span class="str"> country_location (string) : The name of the country the location is in.</span> </span><span class="r"></span></p>
<p id="t117" class="pln"><span class="n"><a href="#t117">117</a></span><span class="t"><span class="str"> folder_name (string) : The name of the folder the location is in, e.g. 'contact_networks'</span> </span><span class="r"></span></p>
<p id="t118" class="pln"><span class="n"><a href="#t118">118</a></span><span class="t"><span class="str"> group_type (string) : The name of the group type.</span> </span><span class="r"></span></p>
<p id="t119" class="pln"><span class="n"><a href="#t119">119</a></span><span class="t"><span class="str"> n (int) : The number of people in the population.</span> </span><span class="r"></span></p>
<p id="t120" class="pln"><span class="n"><a href="#t120">120</a></span><span class="t"><span class="str"> with_ages (bool) : If True, read in the ages of each individual in the group; otherwise, read in their IDs.</span> </span><span class="r"></span></p>
<p id="t121" class="pln"><span class="n"><a href="#t121">121</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t122" class="pln"><span class="n"><a href="#t122">122</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t123" class="pln"><span class="n"><a href="#t123">123</a></span><span class="t"><span class="str"> A list of lists where each sublist represents of group of individuals in the same group and thus are contacts of each other.</span> </span><span class="r"></span></p>
<p id="t124" class="pln"><span class="n"><a href="#t124">124</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t125" class="run"><span class="n"><a href="#t125">125</a></span><span class="t"> <span class="nam">file_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="str">'demographics'</span><span class="op">,</span> <span class="str">'contact_matrices_152_countries'</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_'</span> <span class="op">+</span> <span class="nam">group_type</span> <span class="op">+</span> <span class="str">'_with_uids.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t126" class="run"><span class="n"><a href="#t126">126</a></span><span class="t"> <span class="key">if</span> <span class="nam">with_ages</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t127" class="run"><span class="n"><a href="#t127">127</a></span><span class="t"> <span class="nam">file_path</span> <span class="op">=</span> <span class="nam">file_path</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">'_uids'</span><span class="op">,</span> <span class="str">'_ages'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t128" class="run"><span class="n"><a href="#t128">128</a></span><span class="t"> <span class="nam">groups</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t129" class="run"><span class="n"><a href="#t129">129</a></span><span class="t"> <span class="nam">foo</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t130" class="run"><span class="n"><a href="#t130">130</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span><span class="op">,</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">foo</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t131" class="run"><span class="n"><a href="#t131">131</a></span><span class="t"> <span class="nam">group</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t132" class="pln"><span class="n"><a href="#t132">132</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t133" class="run"><span class="n"><a href="#t133">133</a></span><span class="t"> <span class="key">try</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t134" class="run"><span class="n"><a href="#t134">134</a></span><span class="t"> <span class="nam">group</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">float</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span><span class="op">)</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">group</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t135" class="mis show_mis"><span class="n"><a href="#t135">135</a></span><span class="t"> <span class="key">except</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t136" class="mis show_mis"><span class="n"><a href="#t136">136</a></span><span class="t"> <span class="nam">group</span> <span class="op">=</span> <span class="op">[</span><span class="nam">i</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">group</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t137" class="pln"><span class="n"><a href="#t137">137</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t138" class="run"><span class="n"><a href="#t138">138</a></span><span class="t"> <span class="nam">groups</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">group</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t139" class="run"><span class="n"><a href="#t139">139</a></span><span class="t"> <span class="key">return</span> <span class="nam">groups</span> </span><span class="r"></span></p>
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